Elite Revolution
by plasmasphere
Summary: The Elite Four have found a way to gain far more power than they ever had. RubySapphire based, not anime.
1. Message in a Bottle

August 3, 13 AL (After the Battle of the Legendaries)

* * *

To: All pokémon trainers 

As you know, the Elite Four have recently required anyone who defeats them to take an extra test, but we have yet to see a trainer pass. It requires Champions to be skilled not only in fighting, but also in their ability to catch pokémon. Unfortunately, it is not as simple as they make it seem.

Last year, the Elite Four managed to receive funding from the Hoenn government to send the champion to Birth Island, the site of a recent meteor crash. Sailors who had passed by said the trees had mutated and become misshaped. Some believed a powerful pokémon had taken over, but jagged rocks that had fallen away from the impact surrounded the island and smoke that chokes any flying pokémon still issues from the crater.

The Elite Four made a special cloaked ship for the Champion that would protect him from the smoke. He was sent off with much applause and expectations for the rare pokémon he would return with. A week later, his ship returned, but no one stepped out. The Elite Four carefully walked up to the ship and climbed onto the deck. After a few minutes, one of them saw someone in the hold. Peering in, they saw the champion huddled in the bottom trying to stay hidden. They called to him and he did not answer. When they stepped in to get him, they listened carefully and heard him mumbling over and over again, "The red monkey. Don't let it get me." Sitting beside him was a melted pokédex.

He was given special doctors to cure him, but the paranoia would not subside. Finally, he stopped talking at all. No one could tell what had happened. The Elite Four simply told the public that he had failed and a new champion would be needed to find out what was on the island. They never claimed to have hidden the Champion, but not even his family has seen him since then. The doctors who had gone to help the champion disappeared with him.

I now know why the Elite Four did this. Originally they only wanted to see what the reports from trainers who had surfed by the island meant, but after a week with no Champion they realized something new. With no champion, they were the strongest trainers in the world.

After a few months of repeated tries from many pokémon trainers, a new champion managed to defeat the Elite Four. This could not stand.

The Elite Four then officially declared that there could be no new champion until someone could catch the pokémon on Birth Island. The new champion was sent off like the first to catch it, but the same thing happened to him.

The above is the result of months of research. I have known since I began that I could defeat the Elite Four, but I did not believe that there really was a pokémon on the island that the champions had been sent to catch. I expected that the champions had been locked in a cell in some prison, but last night I saw them. All were locked in an underground cave that has no entrance but by teleportation. I was forced to leave after the Elite Four noticed me. Other than the Elite Four and the doctors who are locked in with the champions, I am the only one who knows what is really happening. I have now defeated the Elite Four and I am the new champion. Tomorrow I will be sent to Birth Island to find the pokémon. If I do not return in two weeks, this message will be released onto the internet so that all can see what the Elite Four are doing. I pray that I will return with this mystery pokémon before then.

Transmission from the Birth Island:

Added August 6, AL 47

I have seen the pokémon. I tried to fight it, but it proved to be a powerful physic very quickly. I could not fight its will and grab a pokémon from my bag. I ran and I think I have escaped, but all my pokéballs seem to be stuck shut. My pokédex identified it as Deoxys, but little information is available until I catch it. I will retur… wait. I hear something behind me. A blue tentac-

-

-

-

_I thought you humans were smart enough to understand my warnings. Obviously I was wrong. Now I must use this puny "trainer," as he calls himself. I am too powerful to be "trained" by a mere human. Instead, I am now forcing him to send this message. Your pokéballs can never hold me. This is the last human I will return to you in the ship normally, albeit with their minds distorted. Any more who try to get me will return and make sure no one is alive to come and disturb my island again. Do not test my wrath._

-transmission ended


	2. Control

August 17, 13 AL

10:30 AM

* * *

Sidney, Pheobe, and Glacia stepped delicately into the Hall of Champions. They peered around the room they had always been near and yet never entered. Tradition dictated that they could not enter this room, but they had already broken enough rules that it did not matter. 

"Get over here, you guys. We don't have all day!" yelled Drake.

"Why the hall of Champions, Drake? We don't need to be so obvious," returned Pheobe.

"Get over it. With that e-mail out from the last champion we sent to Birth Island, we won't have long to wait before trainers start claiming that we have no right to be here at all," answered Sidney.

Glacia added, "He is right. We have no way to prove Alexander's letter false. It came from his official website. How are you planning to keep up the charade, Drake? If people know what has happened, we have no chance here. We have no worthy reasons besides how controlling all those Champions were. Their lording over us will seem normal to most people. They haven't been forced to live through it for years."

"I don't feel like trying to disappear," said Pheobe, "but what choice do we have? Only suppression of evidence has kept it up so far."

"Fine," said Drake, "Hand yourself over to the trainers who are now on their way here. I, on the other hand, plan to defend Ever Grande City. We are strong enough to keep the trainers from having any power. I led us this far, did I not? I used the rumors of Birth Island to get rid of the Champions. You only wished to put the Champion in his place and show that he was not as strong as he claimed. I knew we could be greater. I knew we must be. Now, will you be?" He stared at each of them in turn.

As he looked at Sidney, he answered, "This isn't 'going according to plan,' Drake. We know we need to do something. You better have a plan. We will follow you if you have something we can do." The others nodded in agreement.

"I am glad that you understand. First, we need to stop the immediate threat. Glacia, I need you to go outside and have Walrein start Rain Dance. After you have brought enough clouds, Salamence will use Thunder to keep any flyers away."

"I will begin," answered Glacia, and she turned to leave.

"Wait!" Drake commanded, "After the clouds have been summoned, you need to finish off the last entrance. After the rain has started, the cave can be filled with water and frozen to shut off that entrance."

"I assume that will work. What will Sidney and Pheobe be doing, or am I not allowed to give input to your master plan?" she inquired.

"They shall take care of the more distant dissent. Now go. We need action, not discussion."

She strode away.

"Pheobe, you need to take care of the Champions and those with them. Finsh them off so that no one will know what we have done."

"What?" she exclaimed, "I worried about sending more Champions to Birth Island after the first one came back with his mind destroyed, but killing them? You are going too far. I could hide them better than in that stupid cave of yours. Not all hiding places are far away. No one will find them near here. They do not need to join the dead!"

Drake hesitated, then replied, "I am sorry. I thought too quickly. I have a better idea. You go to the leaders of Team Magma and Aqua. Convince them to come here and meet with me. Tell them I can give them power over all of Hoenn if they will become the Elite police. I do not mean to only be the best pokemon trainers. We need utter control. After that, find the people in the senate who can effect a new rule to give trainers only two pokemon each, not six. Use the same ones we used to enforce the rule about Birth Island. We do not need any more resistance than we already have. The Teams will help with … convincing them."

"Thank you. I'm glad you understand," Pheobe answered, and she left.

"Now for you, Sidney," Drake whispered as she disappeared, "You know we need to finish the Champions. Go and do the job she would not. You love the dark, so let them go into it and never return."

"A good battle," Sidney returned, "I'm tired of telling the people who beat me how great they are. It'll be refreshing to turn the tide and let my darkness destroy them. Would you mind if I gave them an Abra or something to defend themselves with?"

"We are short on time. You may have fun later."

Sidney turned away with a sigh.

"Now I must do my part," thought Drake as he left to begin Salamence's storm.


	3. Friends

August 17, 13 AL

11:48 AM

* * *

"Kyle, get up!" yelled Terra as she knocked on her brother's door. 

"Go away. It's Saturday," he answered, but he looked over at the clock and realized it was nearly noon. Grudgingly, he rolled out of bed and shuffled to the door. As it creaked open, he admitted, "Okay, so it's late. But we weren't planning to do anything today, were we?"

Terra just shook her head as she said, "Alexander just sent an e-mail to everyone. It seems like a joke, but it is from his official site."

"Isn't he on some mission for the Champion test? He wouldn't waste time to send a letter. If he's going to succeed, he better be serious about it."

"If this is real, then it doesn't matter how serious he is. No one can pass the test. I want you to check and see if you think Alexander would really send it. I'll be back in a sec."

Kyle closed the door as she left. As he found clothes and got dressed, he looked around his room at posters he had put up recently. Many of them showed scenes from the recent league matches. When matches became public, the Elite Four were beaten more often because their challengers knew exactly what to expect. Alexander had used this to his advantage, so Kyle now owned a shirt with Alexander's pokémon on it.

Terra then walked back in and threw the letter at Kyle. He sat down on his bed and began to read it.

As he read, Kyle shook his head, "Why didn't Alexander tell us? We should be the first to know."

Terra quietly replied, "Would you have let him go if you knew what he was getting into? No, he wanted a chance to do the impossible." She began pacing back and forth. "He left us here in Fortree, then disappeared before showing up at the pokémon league. We had no contact until he told us he was challenging the Elite Four. We watched it… two weeks ago. He should be back by now. If they are consistent, the Elite Four will declare his failure tomorrow. This letter is probably timed to stop them. Keep reading. I'll see just how many people got this."

Terra hurried outside and began talking to everyone she saw. Luckily, with the addition of e-mail to the PokéNav, trainers began carrying them as often as Pokedexes. Few of the trainers had checked their e-mail, but they checked as soon as Terra told them about the one she had received. It was sent exactly as the address stated, "All Pokémon trainers." None of the trainers were forgotten. When she climbed down to the Fortree pokémon center, the crowd was outside the door from all the people trying to find out if it was real. No one seemed to have any answers, so she trudged back to their house.

Meanwhile, Kyle finished reading and decided to check his other e-mail. He sifted through the junk mail from people who had invented a secret product he needed to invest in and others who thought they had seen the funniest site ever created, but then he found a cryptic message from Alexander.

August 3, 47 AL

To: Kyle

er er ad ye

I etoe te ae hr te hmin ae en hl i m lte t eeyn. ko ta gvn te oain wy ol sn to ay epe hr ad ie h Eie or wrig o oe h Capos wo ut o icue e I ol yu w g tee I hn yu a gt s u wtot en se. h cv i js t te ot o te ek f t Pr. hdna o' b al t tleor i lk m Aaaa, o rn Fyo t dg n I yu o tagt on rm eid h gae akr o te rgnl hmin o wl ht mtl rd Ta i te eln o te opud Yu hud i truh Te otr wl poal b es t fn, u te ae o crd f h Eie or ht hy i te lr we te sw e Mk sr te d nt ae h cac. h rd utn ae l oe te lc.

Hurry!

Alexander

PS Talk to Terra

Kyle shook his head. Alexander had always loved codes. It was usually his way of telling them some secret. Normally, he had some simple substitution like taking the letter behind or in front in the alphabet. Kyle began testing these, but none worked. With "Aaaa" thrown in, any substitution would just be a line of the same letters. Finally, he gave up and threw the paper into the trash.

As Terra walked in, he decided to take Alexander's advice in the post script. "Terra, come look at this. I have another message from Alexander."

Terra ran over and skimmed through the message. "Why does he always need to use a code? You're supposed to talk to me, but I have no clue what it is supposed to say. I guess I can just try all his usual codes."

"I already have," answered Kyle. "Nothing works. Can you remember anything he told you? Some clue he left before he fought the Elite Four?"

She stopped and thought for a minute. She looked around the room for anything he had left when he last visited, but there was nothing. "You have seen everything I have. There was nothing important he told only to me."

"No, all three of us were together… but that doesn't mean he hasn't told you anything since then. Did you look at all your e-mail before you woke me up? Was there a message like this?"

"I never checked. I thought the other one was too important." Kyle printed the message and got up to go get a bite of breakfast. Terra logged in and saw a similar message. It was just as confusing, but not exactly the same. At the bottom, it said "Talk to Kyle." Once again, she went through all his classic substitutions. Nothing worked. It seemed that Alexander had suddenly invented a new code. Many of his old ones were known only to Terra and Kyle. He wouldn't need a new one.

Then Terra began to look at the two letters. Two different letters for people who are supposed to talk to each other. Normally they would only be the same. But together…

She started taking letters alternating between her letter and Kyle's. The first letter from hers, then from his. The second from hers, then the second from his. She continued and a message emerged.

August 3, 47 AL

Dear Terra and Kyle,

I mentioned the cave where the Champions are being held in my letter to everyone. I know that giving the location away would send too many people there and give the Elite Four a warning to move the Champions, who must now include me. If only you two go there, I think you can get us out without being seen. The cave is just to the north of the peak of Mt. Pyre. Shedinja won't be able to teleport in like my Alakazam, so bring Flygon to dig in. If you go straight down from behind the grave marker for the original champion you will hit a metal grid. That is the ceiling of the compound. You should fit through. The doctors will probably be easy to find, but they are so scared of the Elite Four that they hit the alarm when they saw me. Make sure they do not have the chance. The red buttons are all over the place.

Hurry!

Alexander

"Kyle! I figured it out! Come back here!"

He ran back and looked it over. "Well, what are we waiting for? I'll grab Scyther and we can get going. You bring Shedinja and it can provide cover," said Kyle as he began collecting supplies.

Terra paused, then, "Why did he ask us to go? Why not send it to the police? They could save him faster than we could."

"They would call the Elite Four first with this kind of message. They're probably required to check if anything like this is real before they do anything. The Elite Four control the government now. Why do you think this impossible Champion test hasn't been stopped? No, he knows we can do it without telling everyone."

"And he knows we can help him without going for help first. If word got out, they would know exactly what we are doing… Can we really do it?"

"Of course we can. Why else would he send it to us?" Kyle tried to reassure her.

They collected their Pokémon, Pokéballs, and other supplies. Kyle waited as Terra searched for her cell phone. They both knew Mt. Pyre had no reception; energy left over from the activation of the Orbs scrambled any signals from the area. Terra wanted it anyway.

They ran outside and Terra brought out Flygon while Kyle got Scyther. They leaped onto their Pokémon's backs and flew off to Mt. Pyre.


	4. Politics

August 17, 13 AL

1:37 PM

* * *

Agatha appeared on top of the giant Pokémart in Lilycove holding an Abra. While most Abras just teleported to the nearest Pokémon center, Agatha's transport Abras were able to teleport exactly where she wanted them to go. She had been training another one, but its Pokéball was missing when she picked this one up. Unfortunately, meeting the leaders of Teams Aqua and Magma was more important than finding one Abra. Drake had already been attacked. 

Before the awakening of Kyogre and Groudon, both team leaders would have laughed at a vague offer from the Elite Four, but those times were gone. The destruction wrought by the two guardians showed the world how extreme both teams could be. Officially, the doctrines of climate change were forgotten and replaced with simple environmentalism in water and on land. Of course, there were always a few who did not wish to change.

Archie flew down on top of a Pelipper. Agatha greeted him just as the elevator opened to reveal Maxie with a Macargo. Both Team leaders stopped and stared at each other.

"No," said Archie, "Whatever you want, I am not working with him. He will destroy anything you try."

"Me?" replied Maxie, "I've never destroyed ancient cliffs just to add a little bit to the sea. He is the lunatic!"

Archie bellowed back, "The police looked into that cliff explosion; it was just tourists playing with firecrackers. I had nothing to do with it!"

"Stop!" yelled Agatha as she stepped between them, "I know you have your differences, but we need both of you if we are going to get anything done. I would have told you on the phone, but the chances of being overheard were too great. We have things both of you want. The records that were hidden away when your bases were taken over are now in the vaults of the Elite Four. I don't like some of the experiments your scientists were trying, but there is a way for you to get all of that back. The Elite Four need an army, and you already have one. I know that you will not work together, but you will not need to. Archie, you and Team Aqua will guard the water routes and island cities while Team Magma watches the mainland. A resistance is forming based on Alexander's letter, and we need your eyes and ears everywhere to stop it."

"If we answer to you, how can we continue helping the Pokémon? That is our real mission."

"You will have plenty of extra time to spend on that. Pay coming from us will be enough to hire better researchers than the men you have," Agatha explained, "Now, will you join us?"

"Decide now? We need to have a meeting to discuss this. Give us… a week at least."

Agatha looked at her watch. "You have half an hour. By that time I will be telling the Hoenn Senate why I need an army. If you do not enter at the right time, you will not get your records back. Wait outside the doors with your teams, and you will know when to come in and let the Senate see my army. I will see you there."

She then walked over to the stairs and went down. They had enough time to make that easy decision. Neither would admit their love of power with the other one watching. When she reached the bottom floor, she left the building and walked south to the Hoenn Capitol. It had replaced the contest arena when public interest returned to real challenge battles shown on television.

As she walked in the back door, the opening ceremonies were beginning. It seemed like every little town's Senator needed to thank someone before they began any real business. A discussion of fishing rights near Dewford town followed. After it was decided that commercial fishermen could not stop trainers from fishing off the shore, Agatha took the floor. She watched and waited until she had complete silence, and then her speech began.

"We are no longer safe. Pokémon are no longer just for battles against each other. Earlier today, Drake was attacked by a trainer and all six of his Pokémon before he was even allowed time to pull out a Pokéball. As you know, engagement rules dictate that only one Pokémon may be brought out at a time, but we have no way to remotely know whether or not it is a battle. Noman could have survived the attack, but luckily his Salamence was nearby and able to block the attacker before Drake was hurt badly. He held off until Glacia was able to push away this trainer with a Blizzard, and Drake is now recovering from second-degree burns. We now have reason to believe that this trainer was not working alone, and more will follow. They do not only mean to destroy the sacred institution of the Elite Four, but also to replace this Senate with a government of their own choosing. If trainers think it is fine to use Pokémon as weapons, real battles can no longer be conducted. To protect the fair nation of Hoenn, the Elite Four needs military power and emergency executive power to stop these traitors. Allow us this, and we will create an invincible Elite Guard to protect you."

"Where can you get such an army? How do you have time to train it?" asked a Senator from Little Root Town.

"We already have one," answered Agatha, and Teams Aqua and Magma stepped in. "Also, these rebel trainers need to be weakened. After seeing the danger of allowing trainers six Pokémon, the limit for Pokémon held must be dropped from six to two. The Elite Guard will still hold six for their own safety. Given the high probability of rebels attacking again, the Elite Four must also have the full power to do whatever is necessary to stop them. Any rules created will be checked with you as soon as the emergency is over. We question the commitment of anyone who does not think we need these safeguards to defend you and all of Hoenn."

She ended, and a minute later, the Senate had unanimously voted in favor of everything the Elite Four wanted.


	5. Prison Break

August 17, 13 AL

1:42 PM

* * *

Terra's Pokénav finally lost the signal as they neared Mt. Pyre. A trainer calling himself "Firestorm" had announced that he would take on the Elite Four completely alone. If he wasn't already there, he was giving them too much warning. Hopefully, the Elite Four could be stopped while they saved Alexander, but she doubted that Firestorm had a chance. Everyone who could defeat the Elite Four had been hidden ahead of them. 

Flygon stopped flapping and Scyther's buzzing wings slowed down as they neared Mt. Pyre. They landed softly just north of the grave marker. Flygon and Scyther collapsed from exhaustion after an hour of top-speed flying, so Kyle and Terra put them back into their Pokéballs for some rest. With no damage taken, they would recover soon.

"Now we dig," said Terra as she brought out her Sandslash. "Ready, Slash?" she whispered while stroking Slash's back.

Kyle asked, "I still can't believe you do that without getting poked."

"She keeps them soft if you don't try to grab her."

"But you told me to!"

"You should have told her that."

Kyle sighed as he took out a Shedinja and said, "Angel can look down ahead of Slash to make sure she goes the right way. That way Slash won't get tired out by going off a little. Go ahead, Angel."

"It's a ghost of a bug, and you named it Angel," groaned Terra.

"I've told you before; _he_ has a halo and Wonder Guard," replied Kyle. He threw a stick at Angel just before he went underground. When it was a foot away from Angel, it bounced back as a white sphere flashed around the Shedinja.

"Inja," squeaked Angel playfully as he continued into the ground.

Terra and Kyle became quiet as clouds covered the sun.

Below them, Angel floated through the ground listening for any sound. Slash had started digging above him, but he could still hear voices below. Only Angel's eyes entered the room so he could see as well as hear without being seen. Three men in white coats sat around a table.

"Well, he told us to stay here, didn't he? I wouldn't want to anger anyone who's guarded by a Mightyena like that one."

"I just don't like how he said that he would _deal_ with them. Alexander was only trying to help us when he came here the first time."

"But he can't come again. Sydney is our only ticket out of here."

"Hey look, it's a ghost!" After being noticed, Angel decided to leave.

"Third one this week," was the last thing Angel heard.

"Inja, inja!" squeaked Angel as he reached Terra and Kyle. They were following Slash as he dug down. Angel led Slash to make sure she would not run into any of the metal bars in the ceiling. When Slash made it through the roof, the doctors stood up and started to back away.

"Don't worry, we only want to help," assured Kyle.

"Who are you?" questioned one of the doctors.

"We are Alexander's friends and we won't get you in trouble. Instead, you can get out the way we came in. But first, where is Alexander?"

"He is at the end of the hallway, but-"

"Terra, you go, I'll find out more." She left with Slash as he continued, "How is Alexander?"

"I'm trying to tell you that Sydney is already down there!"

Two shots rang out as Terra reached the door, and Kyle began running. First, Terra saw two men dead on the ground. Neither was Alexander. She turned to the right and saw Sydney facing away. At his feet was someone who must be Alexander, but she could barely recognize him. Gashes given by the Mightyena standing over him covered his face and bruises were everywhere. An Abra with ghost-shaped tattoos lay next to him as if it had been knocked away before he was attacked. Sydney kicked him, muttering, "… for getting in our way."

Terra screamed, and Sydney turned around and pointed his gun at her. Slash jumped up to knock it away, but Sydney fired when she did. The bullet went into Slash's left shoulder just as her right claw tore through the gun. It fell to the ground destroyed. Slash fainted and returned to her Pokéball. Sydney ran up and slammed Terra against the wall behind her, yelling, "Tell me, are you alone?"

"NO!" answered Kyle, "Terra, duck!"

She moved her head to the side as a Shadow Ball appeared out of the wall and hit Sydney's head. Angel followed.

"Do not touch my sister!" yelled Kyle as he tackled Sydney. A moment later, he was pulled back off by Mightyena. Angel moved in to help, and Mightyena jumped at him. The Wonder Guard appeared but then turned black as Mightyena went straight through. The moment he touched Angel, Angel fainted and returned to his Pokéball.

Kyle pulled out his Scyther and took Terra's Flygon as she stayed frozen in fear.

Sydney added a second Pokémon to match theirs as he threw out Sharpedo. Scyther started flying forward and Flygon used Dragonbreath, but a Hydro Pump came out of Sharpedo. The fire of Dragonbreath was put out and both Pokémon and their trainers were thrown against the wall next to Alexander. The Pokémon fainted and returned to their Pokéballs.

"You shall not escape," hissed Sydney.

Kyle tried to grab another Pokéball, but Terra stopped him. Instead, she grabbed Alexander and the Abra. Mightyena and Sharpedo charged. Kyle touched Terra and she yelled, "Teleport!"

They disappeared.


	6. Trust

August 17, 13 AL

3:06 PM

* * *

"You have failed, Sydney," intoned Drake. Echoes reverberated around the half-lit Hall of Champions, "And why did you not call sooner?" 

"Drake, I'm sorry, but my phone fried when I tried to use it in Mt. Pyre. If we start searching now, we can find them."

"No, you were too slow. The Elite Guard has already found them. The doctors showed up at the Hoenn television company, but the Elite Guard was guarding it. Unfortunately, they lost the trainer who brought them there. He flew away as soon as he saw he would be overpowered. I just cannot understand how the doctors managed to get out. Would you be kind of enough to explain how they did this?"

Sydney replied, "They did not escape on their own. I was dealing with a pair of kids who must have tunneled in. I only saw them after they tried to save Alexander. I defeated them easily, but they…ah… had an Abra and teleported away."

Glacia walked in and told Drake, "The Kanto Elite Four have heard some bad rumors." Then she saw Sydney, "Oh, am I interrupting something?"

Drake answered, "Stay here, we'll be through in just a minute. I'm just learning of another problem Sydney had." He paused, thinking he had seen someone through the doorway, but no one entered.

Glacia paid him no mind, but questioned Sydney, "Did you lose the Champions too or something? What else is there to screw up?"

"No, I finished off the champions and made Alexander pay for sending his message, but I was seen by some kids. The cowards teleported away."

Drake returned his concentration and started giving orders, "Sydney, I will give you one more chance. Find these trainers and bring them here; we must learn how they found the champions. Glacia, the Kanto Elite Four have heard stories about what we are doing from the wrong sources. You must return there and assure them that what we are doing is necessary."

"Go back? I left because they are _idiots_. I refused their offer for an Elite Four position, and they would not let up. They don't know when to stop. You should go out and do it; I can take care of things here."

"I am an outsider. You were almost one of them. I am sure you can get over this ridiculous feud."

"But… fine, Drake. I will do it your way." Glacia slowly walked away.

After she left, Drake continued, "Sydney, I need you to watch her and Phoebe. I fear that one of them may have questioned what we are doing and betrayed us. Go and find your witnesses before someone else does."

Later, he would tell the same to Glacia and Pheobe. Their loyalty would be only to him as they watched each other.

Glacia was waiting for Sydney outside the door, "I thought we were a team of equals, not Drake and his worthless pawns."

"He is a paranoid control freak. I'm not sure how long I can put up with it," answered Sydney. They became silent again as they walked out.

After they had gone, there was still someone left by the door.

Agatha huddled in the shadows. She shuddered, crying silently. _They lied. He killed the champions._


	7. Hurt

August 18, 13 AL

9:13 AM

* * *

Kyle and Terra awoke with splitting headaches. Blinking from the light, they looked around and saw that they were in two of the beds in the back room of a Pokémon center. As a nurse walked in, Terra realized who was missing. 

"Where's Alexander? Is he all right?" she blurted out.

The nurse replied calmly, "That poor boy who was with you? He'll be fine. Steven is caring for him. I'm not as good with people as I am with Pokémon. You three sure did give me a fright when I saw two trainers unconscious on my scanner. I sent Steven out to get you from the beach, and he left you two here, and said he would take care of your friend. The funny thing, though, is that your Pokémon weren't all unconscious when he found you. That Abra of yours was balanced perfectly on its head. I think it tried to teleport you upside down. How did you manage to train it so badly?"

Kyle groaned, "It isn't ours. I think it was Syd-"

"Kyle!" hissed Terra, "Don't say anything about him."

"Oh, don't worry. I'm supposed to arrest you for attacking Sydney, but either you did a very poor job of it or he attacked first. Either way, neither of you is in any condition to hurt me. But I do wonder about that Abra. When an Abra uses Teleport, it flees to a safe place. When it is wild, that's its den. If it has a trainer, that's here. Do you know why it wouldn't do that?"

"No," replied Terra, "but Sydney could have done something weird. And I can believe he would blame us after what we saw. So why don't you arrest us?"

"My job is to heal anyone who comes in here as long as they won't harm anyone. Officially, I'm also supposed to arrest any other members of Prism who come in, but Steven has made sure I don't need to do that either."

"Other members, Nurse…?" asked Terra.

"Jennifer. Nurse Joy left because she couldn't take their constant fighting, so now it's just me."

"Well, Nurse Jennifer, what is Prism? And what does Steven have to do with it?"

"Prism? You mean you fought Drake, and you had no support?" Nurse Jennifer asked confusedly. Terra shook her head. Nurse Jennifer explained "They oppose just about everything the Elite Four do. Friends of Firestorm, the crazy trainer who attacked Ever Grande City, started it, and I took care of Firestorm after Drake defeated him. Steven has been quietly leading the group here in Mossdeep City. Those Elite Guards- I guess you've been out too long for that too?" They nodded. "They're the Elite Four's private army hired from the last of the Teams. They, on the other hand, were giving a description last night that was definitely you two. Steven had already guessed you would be wanted, so we agreed I would claim you were never seen."

"And you can stop them from checking?" asked Kyle incredulously.

"Prism attacks them regularly, so they need a Pokémon Center. If they tried to force their way in, I would no longer serve them. That would be too much even when they have more Pokémon than everyone else."

"More Pokémon? Do they hold ten or something?"

Nurse Jennifer explained the new rule about only two Pokémon and how it was from a Lanette's central PC, so she could do nothing about it. Terra said that she wanted Slash and Flygon back, and Kyle wanted Angel and Scyther. She explained that the Pokémon were still hurt, but Kyle and Terra would get them back later.

"Now you need to sleep," Nurse Jennifer said, "but just one question before you drift off. I can tell you're brother and sister, but I still can't figure out who is older."

"Me!" answered Kyle.

"He _means_ we're twins."

"I'm still older."

"Fifteen minutes does _not _count."

"Yes it does…yawn."

Nurse Jen turned off the lights and said, "Head injuries require rest. You can add any other comments later."

They were asleep before Nurse Jennifer could walk out of the room. She looked in on their Pokémon. They would be fine by the time Terra and Kyle awoke. She wondered about their friend's name, though. Was he the Alexander who wrote the letter to start this war? That would explain Steven's interest. Of course, how could anyone tell with all his scars? She shuddered at the memory. She would need to ask them when they awoke.

An hour later, she heard beeps coming from her scanner. She checked names, and realized there were six Prism members. Every other time only one or two had blacked out while the others finished the Elite Guards. Someone dangerous was here. She turned and went into the back where Kyle and Terra were to wake them. They might need to leave very soon.

She started to shake Kyle. "Wake up. You need to leave now."

"Leaving? I don't think so, my friend." A voice came from behind her.

She turned to see Sydney with his Mightyena and Absol behind him. "Nurse Jen," he said condescendingly, "I know you are new here, but I thought you understood that this is a _Pokémon_ center. I am sure I can find a better hospital than this crude place. Go ahead and wake them. I won't stop you."

Nurse Jennifer looked back into the other room, wishing she could call for Steven. But she had no choice, so she woke the twins.

Both awoke and tried to grab a Pokémon off their belt when they saw Sydney, but there was nothing there. All of their Pokémon were still being healed. With nowhere to run, they could do nothing but be herded off by the dark master and his Pokémon.


	8. I Have My Reasons

August 18, 13 AL

2:52 PM

* * *

Drake smiled as he stepped into the League's makeshift hospital. 

"Hello, Kyle, Terra," he nodded at each of them.

"I'm going to get you, you filthy-" Kyle was stopped as Salamence's tail slammed down in front of him and forced him to sit down again. Salamence had been guarding them ever since they arrived, but they had seen no people except Sydney and a few Elite Guards.

"Kyle, just stay quiet until we can do something useful," whispered Terra. They had already looked for ways to escape, but there were no windows, and they figured there would be Elite Guards outside the door. Salamence hadn't let them near enough to check.

"I hope you two are enjoying this clinic a bit more than that little place in the back of a Pokémon Center. It must have been quite cramped."

"It was better than being close to you," replied Kyle.

"Kyle, if I wanted to hurt you, you would already be dead. Seeing as you are not, I thought you would want to know why you are here," he paused, seeing that he had caught Terra's attention, "but I can tell that nothing I say will convince you, Kyle."

"Nothing from a black-hearted murderer ever will."

"Terra, if you want to know why you are still alive, I would suggest that we move to another room where your brother will not be insulting me with every sentence. Your alternative is, of course, to be locked away until you change your mind."

"I'm not leaving my brother. Just get it over with; you must be dying to gloat about your evil plan to rule the world."

"Rule the world? Never. Alexander simply forced us to take control so our true mission will not be harmed. Once, all four of us worked together for a more important goal. Now, I cannot trust the others. I fear they may believe that we are here for power instead of our mission to help pokémon by having less be captured. No one ever condemns trainers for capturing pokémon because they know that pokémon will be well cared for by their trainers. But how many can a trainer truly care for? I checked your Pokénavs just enough to see that you are normal trainers: you have a favorite pokémon. It receives most of your attention, the others are there but not as important. You care for them too, but it is not the same. I won't blame you; there just isn't enough time to care for all six the same way."

"We heard that Agatha explained it differently to the Senate. You're just making this up now," said Kyle.

"When Agatha went to the Senate, a bunch of nontrainers, security was the only thing important enough to convince them to make immediate changes. They would never have understood how much care goes into those few pokémon."

"But why have a second pokémon at all? You seem to think one should be the limit," asked Terra.

"It would be nice if we could do that," agreed Drake. "Unfortunately, not every pokémon can transport people, so an extra is needed for flying or surfing. Imagine trying to get around using only your Sandslash. You would be forced to walk everywhere. Also, without trying to spread secondary care among all five, the second will be better treated."

"I don't care about some fake mission," interjected Kyle, "you killed the champions!"

"I never wanted them killed. If your friend Alexander hadn't tried to save them, they would be doing fine. They had everything they needed and were recovering well."

"But you didn't need to hurt them in the first place. They could've avoided all if this if they had never gone there!"

"What do you think would have happened if we had announced that a single pokémon defeated the Champion and no one was allowed near it? Would only the Champion be attacked? No, it would become every trainer's dream to catch the uncatchable pokémon. Remember, your friend Alexander knew about the danger and went anyway. Warning them would not have helped. Instead, they become a symbol of a failed system. A system where thousands of pokémon spend their life uncared for. Also, there are others there only for a trainer's collection in a PC somewhere. Once we have defeated Prism, all those stuck in PC's will be released. And why haven't we done this before? No Elite Four has ever convinced average trainers to voluntarily carry fewer pokémon. They want every advantage they can get in a battle. The original Elite Four thought they could set an example by carrying only five, and that tradition has never been broken. No trainer has ever challenged us on even terms by using only five. They take every advantage they can and use six. Then they have power. Power that comes from being able to sacrifice one of their pokémon to weaken the opponent's best. If you always fought only with your favorite, it wouldn't be much of a change. For them, there is no one that is loved. Instead, all are just there to fight. A champion gives orders and the pokémon follow them. The individuals do not matter. As long as the opponent is hurt worse, it is success."

"No, you never saw Alexander and his Blaziken together. They were closer than any other trainer and his pokémon!" Kyle answered.

"Maybe once he was like that. But he disappeared before challenging us, and there he must have changed. You must have watched our battle. Do you remember the fight between him and me? At the end it came down to his Blaziken and Salamence here." Smoke blew from Salamence's nose in agreement. "They fought with fire and claw, but in the end Blaziken released the strongest Overheat that I have ever seen. That is where the public tape ends. The commentators then jump to an interview later on with Alexander. There are many things you did not see. The metal floor below Blaziken _melted_. When he was returned to the Pokéball, feathers outlining the shape of Blaziken were left stuck in the ground. He actually spent longer in the Pokémon center than Salamence did because he used so much energy. Alexander seemed to be more worried about catching Deoxys than looking in on Blaziken."

There was silence, then Terra questioned, "So what"s the point? What_ is_ your offer?"

"Unfortunately, the other Elites have forgotten our original mission and oppose me when I have the best plans to advance our cause. They want to get rid of me so they can make decisions that will make each of them more powerful. I could remove them to a prison if I needed to, but they are important. They carry out tasks too important for the Elite Guard, and I would need to replace them. You two could learn from me and, one day, bring peace to Hoenn and give full life to all pokémon."

"But why would you offer it to us? You know we will refuse."

"I thought you might see the light. You have seen too much already, so you can't be allowed to leave. Kyle, I was amused to hear stories of your Shedinja. The Elite Four have long known of its special powers, so every one of us can defeat it, but others have not studied as much. Terra, I feel as if I could trust you. I would assume Prism does too."

He turned and left the room. The lock clicked behind him.

"I hate him," muttered Kyle.

"And so do I," answered Terra, "but if he hadn't killed Alexander, I could almost believe him."


	9. Sky Attack

August 19, 13 AL

5:14 AM

* * *

Light shone off Skarmory's wings as it flew over the island it had once called home. There was almost nothing to see, but a few holes in the clouds were enough to navigate the familiar terrain. It seemed that even the Elite Four could not really control Ever Grande City's weather.

Steven noticed the weakness, but it did not matter. Only one thing was in his mind: getting the trainers he had lost back from Drake. They might be his only way of finding out about Alexander. He had given instructions to Nurse Jen about taking care of Alexander, but she didn't know how long recovery would take. Steven only hoped his guess was wrong.

Memories of times training with Skarmory while he was Champion flooded back, and he knew the land below him. He told Skarmory to begin flying in a circle and found another Pokéball. Only one of the five Pokéballs he carried would open if he threw it. He found it and sighed.

He knew what he needed to do.

"Follow me, Skarmory. I will need your help to fix my mistakes."

With that, he slid off and fell into the clouds.

/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l

Salamence paced the room, trying to stay awake. Drake had gone to sleep and left him on guard duty. He went and checked on the twins. They awoke as he walked between their beds, then turned away. He continued back toward the door.

Crash! The ceiling collapsed and pieces fell. Terra screamed, but then the pieces above the twins stopped in midair and moved away to reveal Metagross.

As Salamence pushed the piece back off, he was hit by a Psychic. They looked and saw Metagross standing in the center of the room. Steven came down from the sky, slowed by Metagross' Psychic. When he hit the floor, he ran toward the twins.

"Come on," he whispered, "we leave now."

Across the room, Salamence began to get up. He looked up, and saw Skarmory. A Dragonbreath left his mouth, but Skarmory turned to the side just as it swirled past. Steven pulled the twins along with him as he jumped under Skarmory's new position. They looked back as they grabbed onto the silver Pokémon. Metagross had Salamence pinned underneath him, but Salamence was flapping the one wing he had free.

"Metagross, quick!" yelled Steven.

Metagross pulled a chunk of the ceiling toward himself with Psychic, then jumped up. The concrete slammed into Salamence.

Just as Metagross reached the top of its jump, Skarmory swooped over. Steven held out a Pokéball and Metagross disappeared into it.

As they flew higher with no sign of being followed, Kyle sighed, "That was close."

Then Salamence roared.

Everyone in Ever Grande city awoke. They would be followed.

"We're definitely not out yet," Steven said.

Sunlight bathed the three trainers as they exited the clouds. As their eyes adjusted to the light, cawing came from behind them. Thirty seconds later, a flock of Murkrow rose out of the clouds. At its center sat Sydney on a massive Murkrow. Behind him came Drake on Altaria with Salamence at his side, all with blinding sunlight behind them.

"Take these, we need them now." Steven handed two Pokéballs to each of the twins. "Nurse Jen told me these were the ones you would want, and Skarmory can't carry all our weight for long."

Terra brought out Flygon and leaped on. Flygon tried to turn her head enough to look back and shoot a Dragonbreath, but she couldn't quite reach.

Kyle brought out Scyther who caught him as he nearly failed to jump on. Shedinja materialized next to him and began firing Shadow Balls back at the flock of Murkrow.

The flock just moved away every time one came near and none seemed able to hit. The sun in Shedinja's eyes didn't help either.

After watching their failures, Steven reluctantly brought Metagross back out. Skarmory strained to carry the extra weight. "Metagross, use Levitate! Skarmory isn't that strong!" Steven groaned. Metagross used Levitate and Skarmory grabbed on with its claws to keep Metagross moving. After they were set, Steven commanded, "Meteor Mash!" They waited a moment for something to happen. Then a Murkrow disappeared in a puff of feathers. Looking up, the rest realized that flaming meteors had begun to fall from the sky. The rest of the rocks were dodged by the small birds. Salamence and Altaria just blasted anything that came near then with Dragonbreath.

Nothing seemed to be working. The Elites knew it was only a matter of time before they would catch up with the tiring Pokémon.

Then a thought popped into Terra's head. "Wait a second! Sandstorm!"

A ball of sand burst off Flygon. The Elites disappeared from view as the sand spread out.

"Now attack!"

Shadow Balls flew back in rapid succession and dots of meteor fire appeared high in the sky.

Sand, stone, and shadow hit as one.

All but one of the Murkrow fell down as the storm washed over them. On that one sat Sydney. Drake appeared unscathed.

The three trainers released another barrage, but Sdyney and Drake dodged everything. Even the best idea seemed to fail. But then…

"No, Metagross!" yelled Steven, but it was too late. Metagross had already jumped.

As Sydney opened his eyes after clearing off the sand, he saw only a flying metal Pokémon. Metagross rammed into him. Claws slashed again and again at the Murkrow. It began to fight back, but it stopped flapping and began to fall.

Drake shot down after them and returned the slower Salamence to its Pokéball.

A light flashed as Metagross returned to its Pokéball unconscious.

Terra looked ahead and was startled to see a tower on an island in the middle of the ocean.

"What is that?"

"Safety."

/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l

Drake saw Sydney splash into the water, then pop back up. "Wait there," he yelled, "I shall return after I have captured them." Sydney had enough strength to get out Sharpedo, and it began to push him toward the land. But it felt something in the depths below.

/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l/l

Steven and the twins landed atop the tower.

"Where are we?" asked Kyle.

Steven waited a minute to catch his breath, then began to answer, "Sky …" he stopped as something clattered onto the ground. It was a Pokéball.

Flash! Salamence popped out as Altaria appeared over the low wall. Both opened their mouths and released a Flamethrower.

The trainers jumped behind Skarmory and Flygon hoping they could be shielded from the blast.

Suddenly, a green blur appeared.

The attack disappeared into plates of armor.

It slithered through the air. Altaria and Salamence were thrown back as it hit them. They tried to surround it and both use Dragonbreath, but it shot to the side. Its tail whipped out and knocked Salamence back.

All three flew up, searching for a mark. Dragonclaws seems to be everywhere, the claws of the new Pokémon slashed at anything near its head. It shot toward Salamence, but Altaria was able to blast it from the side. It convulsed and only one claw hit Salamence. Patterns like dragons' Outrage appeared as it turned back. Altaria was hit in the wing, and Drake turned down and away. Salamence shot a Dragonbreath out while the dragon was facing away, and it blasted into the green scales. The body seemed to fall as it dove under Salamence, but then its tail shot up at the end and whipped out. Salamence was thrown back. As he recovered and looked for where the dragon had gone, he was hit by a blast of Dragonbreath. He fainted as he fell and disappeared in a flash of light.

The green dragon slowed as it returned to the tower.

"I was hoping you were around, Rayquaza," Steven said happily.

A deep voice filled their minds. _'And I am glad you are here; I require your help. Something is wrong outside of my domain, but it seems to affect everything in this world. I cannot control its power like I did with Kyogre and Groudon. They change only the weather, but it changes all life around it, and its creations have begun to spread toward us.'_

"Deoxys," whispered Steven. He had known they would need to deal with it eventually.

* * *

Author's notes: So, is a battle in the air better than one in a boring open arena?

Sorry it took so long, but updates should come more often now. Please leave any suggestions in a review, I'll probably use them.


	10. Darkness

August 19, 13 AL

7:26 AM

* * *

Sydney clung to Sharpedo's dorsal fin as it swam toward the island. His eyes were squeezed shut keeping out the salt. His teeth clenched from pain; everything seemed to hurt. He coughed, and it felt like spikes were being driven into his chest. Shards of memory pierced his mind, then drifted away. Memories could not be held onto. Why was he here? Why did it hurt? Thinking hurt. Don't think. Just hang on. Sharpedo is safety. 

Sharpedo felt a shock on his left side; he turned and bit. The Tentacool shot away. Sydney grabbed on tighter, trying not to be shaken off. A few seconds later, another shock came on his right. He turned to defend Sydney, and the Tentacool swam away. Then another came. And another. None of the Tentacool could defeat Sharpedo alone, but he was getting tired from fighting the Tentacool and carrying Sydney. But the land wasn't far. Only a bit farther.

Tentacles wrapped around Sharpedo's tail fin. He turned to fight, but more and more tentacles wrapped around. He bit a few in half, but more came. It seemed like more than even the Tentacruel he had fought years ago while exploring underwater caves with Sydney, searching for other dark water Pokémon. Poison barbs had gone in, and they began to take an effect. Sharpedo's movements slowed.

The shock of stings brought Sydney back to consciousness, and he looked up to see dragons fighting. Even as the two tried to fight against the larger one, it was able to dodge while fighting back. The largest defeated the one with a trainer on it, and the defeated dragon began to fly toward him. The other fell back a moment later. Sydney's hand slipped off Sharpedo. Darkness surrounded him. Sydney's hair lit on fire as Dragonbreath blasted at the Tentacruel. He felt nothing.

Tentacruel dragged its prey down, and they disappeared into the depths. Dragonclaws hit tentacles, and Tentacruel released one of its prey. The giant jellyfish Pokémon didn't fight back; one would be enough for a meal.


	11. Fears

August 19, AL 47

7:28 AM

* * *

_Who are these children? Why are they with you, Steven? They will only slow us down._ Rayquaza's thoughts echoed in the trainers' minds. 

"They are Kyle and Terra, friends of mine. They were very helpful getting here, and I think they could help again."

_Helpful? If I had not saved you, you would be burning like marshmallows left in the fire too long. Steven, just let me carry them home so you can deal with Deoxys._

"NO," yelled Kyle, walking forward. Rayquaza just looked down; even curled up he still towered over any human. "I will help fight Deoxys. That monster nearly killed my friend, and I will make it pay. I will not be left behind."

"This is why they can and will help," whispered Steven as he came closer to Rayquaza, "They care about Alexander."

_So Alexander was their friend? And where are the friends of the other trainers who Deoxys attacked? They are trying to fight the Elite Four and failing. It does not matter how much they care. They are not strong enough. Alexander was a champion. Kyle, you are not. What makes you think you can do any better than he did?_

"Then why should Steven go? Won't he do just as badly? I have as much chance as he does!" Kyle slammed his hand down on one of the rocks.

Rayquaza floated into the air above Kyle. _Why do you question my judgment? I have spent millennia guarding this world; no one has seen more than I. Steven has far more experience than most humans because he has been a Champion. You are not a champion, and I greatly doubt that you will ever be one. Rash actions from a child will not defeat the most powerful Pokémon that I have ever encountered. Deoxys has already shown that it does not care whether the enemy is a human or a Pokémon, they will be eliminated. You would not survive the encounter. It guards its island jealously and no one who enters leaves again. Even if you were much stronger, I would still refuse to have you go. Only a wise trainer will be able to anticipate its moves and gain victory._

"Rayquaza," answered Steven, "I will only help if these two come with me. They do not yet have the experience that I do, but I can teach them. They will help. Trust me."

_Trust you? I know far more about this Pokémon, and I assure you that they cannot help._

"But who found a trainer for you to go into the Cave of Origin? You know Pokémon, but I know people. These two will help."

Rayquaza returned to the ground. _Then I had no choice, and you seem to give me no choice once again. But I implore you, test them more than you have. Many trainers seem to have great potential, but there is really nothing there but a love of competition. Then if you decide that they will not just hurt themselves and your mission, they may accompany you._

"Wait," Terra spoke for the first time, "This isn't really helping us. We've already saved Alexander, but the real threat is that the Elite Four will find him again, and we will have failed at what really matters to us. Defeating this Deoxys could be a wild goose chase; it will only prevent from dealing with the Elite Four. I'm not going to leave Alexander to their mercy."

Steven sighed. He turned toward Terra and replied, "The Elite Four only have power because most people are too scared that they control Deoxys and could use it as a weapon. If we can defeat Deoxys, then far more people will join with Prism and together we can defeat the Elite Four. With the forces we have now, we cannot defeat them. I am not as fast as I once was, so now I cannot win."

"I have a better idea. Rayquaza, how far is it to Deoxys' island?"

_I could fly there in a week, but it will take you much longer. If I joined you, Kyogre and Groudon might have come back out and their destruction would be far worse than anything these Elite Four can do._

"By the time we return, who knows what the Elite Four could do? It only took them a few days to take over the government completely. Wait... There is a way to make this work. Rayquaza, you could help us."

Rayquaza's eyes narrowed as he looked at Terra.

_How?_

Terra talked very quickly, "As you saw, we couldn't even defeat two of the Elite Four. Drake nearly killed us, _but_ then you came and fought two dragons at the same time. If you help us attack them now, together we could defeat them. Think about it. The last thing Drake would expect after chasing us all the way here is an attack on his own sanctuary. He's just fought you once, so he can't do it again today. Sydney was beaten by Metagross, so he won't be ready to fight again either. The three of us can fight Phoebe and Glacia, and you can join in after Drake has nothing left to fight with." A grin spread across Terra's face as Rayquaza searched for an answer.

_It would just be safer to follow my plan and deal with Deoxys first. Deoxys must be defeated, and I will not take any unnecessary risks of that not happening. You are creating too much danger that could be avoided by getting help from other trainers and not counting your own strength._

"But after you help us, we will not be rushed to return back from defeating Deoxys. 'Rash actions' will not happen if we have plenty of time. All of us will be rid of our problems."

"I think she makes a good point. Don't you, Rayquaza?" asked Steven.

"We can't lose. I won't let it happen," added Kyle.

_Fine. The end of Ever Grande City draws near._

* * *

A/N: To quote Gandalf the Grey: "I was talking aloud to myself. A habit of the old: they choose the wisest person present to speak to; the long explanations needed by the young are wearying." 

Please review!


	12. War

August 19, AL 13

11:32 AM

* * *

Ever Grande City grew closer as Rayquaza and the three trainers sped toward it. The clouds disappeared as Rayquaza came near them. Sun shone down, and they saw Drake and Glacia below them. 

Glacia's Walrein shot an Ice Beam up at Rayquaza. Kyle threw his Shedinja out, and the Ice Beam stopped as the Wonder Guard flashed around it. Flamethrower came from Salamence and Rayquaza slid in front. Dragonbreath was blocked by Shedinja. Then the trainers felt their hair stand on end.

"He's using Thunderbolt!" warned Terra, "Go, Slash!" Slash left the Pokéball and fell toward Salamence. An enormous bolt shot out, but was grounded by Sandslash as she landed.

Rayquaza sped down; then stopped inches from the ground. The dying grass crackled as the trainers landed on it.

"Drake, it is time for this to end. Give up now and Rayquaza will not hurt you," threatened Steven.

"Well, not too badly," added Kyle.

"No, you do not understand," replied Drake, "I have uncovered secrets that make me invincible. You shall die."

_Not if I kill you first. _Rayquaza sped toward Drake. Drake spun and threw out a ball. Rayquaza laughed, he was not even hurt.

Then a flash, and Rayquaza was in the ball. It began rolling around in circles, but it stayed. Rayquaza was caught.

"I told you I could not be defeated. You see, in the plans we took from the Teams, I found blueprints for the Master Ball. As you can see, it worked." Drake cackled as he picked up the ball off the ground. "Go, Rayquaza!"

Rayquaza appeared from the Pokéball. _No, I will not fight for you. _

"But you must. Use Dragonbreath on Steven, now!"

_I will not. Drake, I... NO. I don't want to... Ahhhhh..._

A screech pierced the mind of everyone there. It sounded like a million voices all in pain, dragged into a torture chamber. Its intensity increased; then stopped like the door had been closed. Rayquaza turned toward Steven.

An inferno shot from Rayquaza's mouth. Steven disappeared as the twins jumped to the side. They looked back, and saw nothing but a pile of cinders. Rayquaza's tail swung to the side and caught Kyle. He flew back and over the edge of the cliff.

"No!" screamed Terra as she ran toward the edge. She looked over and saw Kyle on the beach, unmoving.

Just then, Phoebe walked out and saw Deoxys coming from behind Drake.

"What is that thing?" Phoebe pointed.

Drake turned to see the Pokémon floating toward him. "That... must be Deoxys. How did it get here?"

_I felt the barriers around this place fall. Something powerful was captured, and I have come to take its place._

Drake stepped back in fear, the smiled. "You will be captured just as Rayquaza was! Go, Master Ball!"

The Master Ball sped toward Deoxys, but was stopped by Deoxys' Psychic. It hung in the air, trying to reach Deoxys but unable to move forward.

"Rayquaza, distract it! Use your Extremespeed to get its attention!"

Rayquaza flew down, but was deflected with another blast of Psychic before reaching Deoxys. The Master Ball moved closer, but still could not suck Deoxys in. Rayquaza came back, but this time Deoxys was ready and the ball only moved a few centimeters.

"Rayquaza, you are a legendary! How can this thing defeat you?"

_Deoxys is like me, but not from here. It comes from a place not of this world. You have restrained me so I cannot use the powers you want._

Terra walked up to the Master Ball suspended in the air. She stared at it for a moment deciding what to do. She reached out to take it. Her hand was millimeters away when she stopped to ask, "Deoxys, why did you attack the Champions?"

_I was only defending myself. They would have held me against my will as Rayquaza is held now. Do you see what has happened to him? That is what I would be. A tool in the hands of power-hungry trainer. Get rid of that ball, and I will help you defeat this man. Trust me._

"Fine." Terra grabbed the ball. She felt the pull toward Deoxys first disappear, and then Deoxys released his push.

She walked toward Deoxys with the Master Ball still in hand. "I want to believe you are good, but..."

Terra lifted the Master Ball and let go. Deoxys was less than a meter away, and the ball opened instantly. Deoxys disappeared in a flash of light.

"Now earn that trust! Go Deoxys!"

She threw the ball and Deoxys reappeared.

_Stupid girl. I would have helped before. Now I must, but it is no longer my own cause._

"Let it be. If we win, you will be released. If he wins, I am sure he will never trust you no matter what you do."

_I hope that you will hold to that. I can make myself useless to you if you try to break that promise._

Rayquaza was coming back. This time he spiraled forward to stop any simple deflection.

Deoxys reached over to the grass on the ground. It turned a violent shade of red. As Rayquaza came closer, it began to grow before their eyes. Just seconds later, everyone was hidden in the high grass. Rayquaza had nothing to hit.

"Burn it where they were! Just don't hit here!" yelled Drake as he jumped up to tell Rayquaza where not to burn.

The spot where Deoxys had been was incinerated, but Rayquaza found nothing. It flew up to be able to see them from above. Deoxys and Terra had moved next to Drake. Rayquaza told Drake, and he began to move away.

Deoxys saw that it would not last long, and fire from Rayquaza would not be stopped by Psychic.

_Not here._

To Drake and the other Elites, it looked like Deoxys and Terra teleported away. But Rayquaza saw them move. They had gone into Victory Road.

_I follow._

Rayquaza shot after them as the red grass withered. Drake ran as fast he could. He needed to see what would happen in the cave.

Glacia and Phoebe followed him. Their eyes were on the Master Ball that held Rayquaza.

In Victory Road, Deoxys turned a corner and found a Lairon. It charged toward him on sight, but he reached out with an arm. When it was touched, it slowed and a glazed look came over its eyes. It lay down, and its metal plate began growing. As Rayquaza turned to see it, the entire corridor had been sealed.

Deoxys let go as the shell turned red hot from the heat of Rayquaza's fire.

Terra followed Deoxys until they reached water.

_Jump in. I'll catch up._

Terra leapt into the river and was quickly pulled toward a waterfall. She looked back to see Goldeen all around Deoxys, but they didn't seem to change like the Lairon.

Fire appeared. Rayquaza entered, but was quickly covered in water thrown up by Deoxys' Psychic. Rayquaza laughed. Water would not hurt him. He looked for Deoxys; then felt a shooting pain in his side. He turned to see a Goldeen with overgrown teeth stuck into his side. He bit it away, but then another came. He was surrounded by biting Goldeen. He shook, but they would not come off.

Deoxys came out of the water just as Terra was going over the waterfall. They flew out and went over to land. They saw Rayquaza pop out over the waterfall covered in Goldeen. He started banging against the walls, and they fainted and fell back into the water.

Ahead was a bridge. Deoxys ran forward and jumped off. Terra dove to the side to avoid Rayquaza as he followed.

Deoxys hid behind rocks and threw anything it could with Psychic. Rocks, water, and Pokémon flew at Rayquaza. It dodged them all, but could not keep up with Deoxys' meandering running below the bridge.

The Elites appeared behind Terra, and she began running across the bridge. She jumped forward to the end as a Hariyama with eight arms flew past.

Drake followed on the bridge but tripped on one of the logs making it up. As he got up, both Glacia and Phoebe grabbed at Rayquaza's ball. They reached it at the same time and tried to snap it off Drake's belt.

Thoughts from all three trainers hit Rayquaza, and it could not think. It began to flail. The bridge snapped as Rayquaza hit it. The Elites all tried to hold on even as they fell. Rocks fell from every wall as spasms shot through Rayquaza. A hole broke in the ceiling, and boulders crashed around the Elites. Rayquaza was hit by boulders it had knocked down and landed atop the Elites. All were covered by the landslide.

The rocks above Deoxys and Terra were tossed away by Deoxys as the scene began to clear. He reached into the pile with Psychic and pulled out the Pokéballs from Drake, Glacia, and Phoebe.

_The Pokémon were saved by the Pokéballs, but the others are dead. And... _He reached out with Psychic to the north. _Your brother is dead, but I will bring you his Pokémon._ Two Pokéballs came in through the hole in the cave and landed at Terra's feet._ Now will you release me?_

Terra shook her head, "I never knew how much pain being controlled by a trainer could cause you. I need your help, but I'll give you a choice."

Terra opened all the Pokéballs she had been given, including Deoxys' and her own.

"No Pokémon should be forced to stay with a trainer. Slash, Flygon, you'll stay with me, right?"

They nodded and rubbed up against Terra. Scyther and Angel came toward her as well.

"I will release all the Pokémon in the world. Those that want to stay with their trainers will stay, the others may leave."

_Thank you, _Rayquaza added, _I will help. Nothing should be held as I was._

_You will have my help, but then I shall return to my island, _Deoxys gave his support.

The Pokémon and their friend rose out of the ruins of Victory Road to release all.

* * *

Next chapter is an epilogue! 


	13. Epilogue

March 3, AL 15

11:32 AM

* * *

Deoxys looked above his trees to see a Flygon gliding down. Terra was visiting again. 

The Flygon landed and Terra hopped off. "Your trees always worry me, I think they're going to turn and grab me or something like that."

_You know that they are fine with you. They have also relaxed since those stupid botanists tried to cut one of them down._

"The botanists just need something to do now that I've stopped them from testing grass Pokémon. It took a while, but I think they've found better things to do."

_Come over to see these new arrivals. This Mightyena will love the pink stripes I gave it, it's so much better than the black and blue it associates with Team Aqua._

"I remember when we found the Elite Guard. It was relieving to see their Pokémon turning on them. I was worried that I had made a mistake after those first few trainers who had Pokémon that wanted to stay with them but were too big. I felt like I hadn't helped anyone."

_The Choice Balls that Lanette helped create were important. How is the Hoenn Senate doing with your ban on catching any Pokémon?_

"The knowledge that you and Rayquaza are on my side basically shuts them up. I've been able to get them to do a few important other things too. Don't worry; it's nothing you would even care about. Now, let's see this new Mightyena you've been working on. I want to make sure she likes it. Remember when you gave Angel horns?"

_That was only a joke. I am sure she will when she wakes up. And you know I can always change it back just like I did with Angel._

The two friends walked off to see the effects on the genetically changed Pokémon that would never become part of a collection.

* * *

A/N: That's it. Review to tell me what you think of the ending. 

Thanks to my Betas Dualwielder and Nolaquen265!


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